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11 February 2011 Functional nanoscale imaging of protein surfaces
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The paper presents an image-oriented modality to functionally describe artificially and biologically nanostructured surfaces, which can be used for the characterization of the atom neighborhoods on the surface of proteins. The property which is mainly analyzed in this paper is the hydrophobicity distribution on protein surface, but the distributions of charges and mutual electrical potentials can also be considered. The actual discrete hydrophobicity distribution attached to the atoms that form a surface atom's vicinity is replaced by an approximately equivalent hydrophobicity density distribution, computed in a standardized octagonal pattern around each atom. These representation of hydrophobicities is used to compute the resemblance of surface atom neighborhoods belonging to a protein, defined as the sum of the products of hydrophobicity densities of the corresponding patches (the pattern's central circles or angular sectors having the same position). The similitude and the interaction of a pair of atom neighborhoods are defined as their resemblance for parallel, respectively, anti-parallel orientations of the normals on the molecular surfaces in the points where the central atoms are located. The purpose of this work is to create a database of selected protein surfaces that will be used for nanotechnology research and applications purposes.
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Paul Dan Cristea, Rodica Tuduce, Octavian Arsene, and Dan V. Nicolau "Functional nanoscale imaging of protein surfaces", Proc. SPIE 7908, Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications VIII, 79080L (11 February 2011);

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